Skip to content
Snippets Groups Projects
Verified Commit 29d92d03 authored by Mia Croiset's avatar Mia Croiset
Browse files

update json schema

parent b6a84d53
No related branches found
No related tags found
No related merge requests found
......@@ -151,7 +151,7 @@ params {
hicstuff_centro_file = 'None' //give absolute path or 'None'
hicstuff_base = 1.1
hicstuff_distance_out_file = 'distance_law.txt'
hicstuff_rm_centro = 'None' //int or 'None'
hicstuff_rm_centro = 'None' //string number (ex: '30') or 'None'
hicstuff_distance_plot = 'false'
hicstuff_distance_out_plot = 'plot_distance_law.pdf'
hicstuff_filter_pcr_out_file = 'valid_idx_pcrfree.pairs'
......
......@@ -526,6 +526,176 @@
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
}
}
},
"hicstuff options":{
"title": "Hicstuff options",
"type": "object",
"description": "Options for hicstuff workflow, set in the config file.",
"help_text": "These options are specific to the hicstuff workflow and allow you to customise the parameters",
"properties": {
"workflow": {
"type": "string",
"description": "Selection of the workflow to run. Choices are hicstuff or hicpro",
"default": "hicstuff",
"fa_icon": "fas fa-cogs"
},
"hicstuff_bwt2_align_opts": {
"type": "string",
"description": "Parameters for bowtie2 alignment",
"default": "--very-sensitive-local",
"fa_icon": "fas fa-cogs"
},
"hicstuff_min_size": {
"type": "integer",
"description": "Minimum contig size required to keep it",
"default": 0,
"fa_icon": "fas fa-cogs"
},
"hicstuff_min_qual":{
"type": "integer",
"description": "Minimum mapping quality required to keep a pair of Hi-C reads",
"default": 30,
"fa_icon": "fas fa-cogs"
},
"hicstuff_circular": {
"type": "boolean",
"description": "Use if the genome is circular",
"default": false,
"fa_icon": "fas fa-cogs"
},
"hicstuff_bin": {
"type": "integer",
"description": "Binsize for plotting matrix",
"default": 10000,
"fa_icon": "fas fa-cogs"
},
"hicstuff_output_contigs": {
"type": "string",
"description": "Name of info contigs file",
"default": "info_contigs.txt",
"fa_icon": "fas fa-cogs"
},
"hicstuff_output_frags": {
"type": "string",
"description": "Name of fragments list file",
"default": "fragments_list.txt",
"fa_icon": "fas fa-cogs"
},
"hicstuff_valid_pairs": {
"type": "string",
"description": "Name of valid pairs file",
"default": "valid.pairs",
"fa_icon": "fas fa-cogs"
},
"hicstuff_valid_idx": {
"type": "string",
"description": "Name of valid pairs index file",
"default": "valid_idx.pairs",
"fa_icon": "fas fa-cogs"
},
"hicstuff_matrix": {
"type": "string",
"description": "Common name of matrix files",
"default": "abs_fragments_contacts_weighted.txt",
"fa_icon": "fas fa-cogs"
},
"hicstuff_plot_events":{
"type": "boolean",
"description": "Whether plots should be generated at different steps of the pipeline",
"default": false,
"fa_icon": "fas fa-cogs"
},
"hicstuff_frags_plot": {
"type": "boolean",
"description": "Whether fragments plot should be generated",
"default": "false",
"fa_icon": "fas fa-cogs"
},
"hicstuff_frags_plot_path": {
"type": "string",
"description": "Name of fragments plot file",
"default": "frag_hist.pdf",
"fa_icon": "fas fa-cogs"
},
"hicstuff_pie_plot": {
"type": "string",
"description": "Prefix of distribution plot file during filter events",
"default": "distrib",
"fa_icon": "fas fa-cogs"
},
"hicstuff_dist_plot": {
"type": "string",
"description": "Prefix of distance plot file during filter events",
"default": "dist",
"fa_icon": "fas fa-cogs"
},
"distance_law": {
"type": "boolean",
"description": "If True, generates a distance law file with the values of the probabilities to have a contact between two distances for each chromosomes or arms if the file with the positions has been given. The values are not normalized, or averaged.",
"default": "false",
"fa_icon": "fas fa-cogs"
},
"hicstuff_distance_out_file": {
"type": "string",
"description": "Name of distance law table file",
"default": "distance_law.txt",
"fa_icon": "fas fa-cogs"
},
"hicstuff_distance_plot": {
"type": "boolean",
"description": "Whether distance law table should be plotted",
"default": "false",
"fa_icon": "fas fa-cogs"
},
"hicstuff_distance_out_plot": {
"type": "string",
"description": "Name of distance law table plot if hicstuff_distance_plot is true",
"default": "distance_law.txt",
"fa_icon": "fas fa-cogs"
},
"hicstuff_base":{
"type": "number",
"description": "Base use to construct the logspace of the bins for distance law",
"default": 1.1,
"fa_icon": "fas fa_cogs"
},
"hicstuff_rm_centro": {
"type": "string",
"description": "If the distance law is computed, this is the number of kb that will be removed around the centromere position given by in the centromere file",
"default": "None",
"fa_icon": "fas fa-cogs"
},
"hicstuff_centro_file":{
"type": "string",
"description": "If not None, path of file with Positions of the centromeres separated by aspace and in the same order than the chromosomes",
"default": "None",
"fa_icon": "fas fa_cogs"
},
"filter_event": {
"type": "boolean",
"description": "Filter spurious or uninformative 3C events. Requires a restriction enzyme",
"default": "false",
"fa_icon": "fas fa-cogs"
},
"hicstuff_valid_idx_filtered": {
"type": "string",
"description": "Name of filtered valid pairs index file",
"default": "valid_idx_filtered.pairs",
"fa_icon": "fas fa-cogs"
},
"filter_pcr": {
"type": "boolean",
"description": "If True, PCR duplicates will be filtered based on genomic positions Pairs where both reads have exactly the same coordinates are considered duplicates and only one of those will be conserved.",
"default": "false",
"fa_icon": "fas fa-cogs"
},
"hicstuff_filter_pcr_out_file":{
"type": "string",
"description": "Name of pair file after PCR filtering",
"default": "valid_idx_pcrfree.pairs",
"fa_icon": "fas fa_cogs"
}
}
}
},
"allOf": [
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment